Digital Nucleic Acid Memory: Synthesizing DNA Scafold and Electrophoresis Optimization

DNA origami offers a high-potential platform for long-term, high-density data storage due to DNA’s exceptional stability, information density, and ability to fold into precise nanostructures. The efficiency of this process depends on both the quality of the single-stranded DNA (ssDNA) scaffold and the conditions used to analyze folded structures. This project combines two approaches to improve the DNA origami workflow. PCR amplification with multiple primer sets was used to characterize the P11453.1 ssDNA scaffold, revealing retained M13 phage genome segments. These contaminants likely contribute to unexpected agarose gel bands and misfolded L-shaped nanostructures. To optimize analysis, agarose gel electrophoresis conditions were tested with varying MgCl₂ concentrations and voltages to reduce run time while preserving structural integrity. Gels run at 80V with 6–8 mM MgCl₂ produced sharp bands and preserved structure, while higher voltages and MgCl₂ levels of 10 mM or more led to smearing and diffusion. These results highlight the importance of scaffold purity and gel optimization for accurate, efficient folding and visualization of DNA nanostructures. Together, these improvements strengthen the reliability and speed of digital nucleic acid memory (dNAM) workflows.